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Limma\'s roast() does not accept weigths in combination with block

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Dear All, I am conducting enrichment tests using Limma's roast() function. As I am investigating RNA-Seq data, I have to introduce the weights calculated by voom(). Without a blocking variable, roast() runs without an itch but when I introduce a blocking variable (with or without correlation within blocks), roast() halts and returns "Can't use block with weights". Is the combination of weights and blocking variables in roast() generally impossible and if not, will it be possible in upcomming releases of limma? Thank you very much in advance, Moritz -- output of sessionInfo(): sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel splines stats graphics grDevices utils datasets [8] methods base other attached packages: [1] DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.20.0 [5] BiocGenerics_0.6.0 statmod_1.4.17 edgeR_3.2.3 limma_3.16.5 loaded via a namespace (and not attached): [1] annotate_1.38.0 AnnotationDbi_1.22.6 compiler_3.0.1 [4] DBI_0.2-7 genefilter_1.42.0 geneplotter_1.38.0 [7] grid_3.0.1 IRanges_1.18.1 RColorBrewer_1.0-5 [10] RSQLite_0.11.4 stats4_3.0.1 survival_2.37-4 [13] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 -- Sent via the guest posting facility at bioconductor.org.

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ADD COMMENT • link updated 11.3 years ago by Gordon Smyth 51k • written 11.3 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2013-08-06

> Date: Mon, 5 Aug 2013 03:36:49 -0700 (PDT) > From: "Moritz Hess [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, ssehztirom at gmail.com > Subject: [BioC] Limma\'s roast() does not accept weigths in > combination with block > > Dear All, > > I am conducting enrichment tests using Limma's roast() function. As I > am investigating RNA-Seq data, I have to introduce the weights > calculated by voom(). Without a blocking variable, roast() runs without > an itch but when I introduce a blocking variable (with or without > correlation within blocks), roast() halts and returns "Can't use block > with weights". Is the combination of weights and blocking variables in > roast() generally impossible Not impossible, but requires some careful special case programming. > and if not, will it be possible in upcomming releases of limma? Yes, but not in the next few weeks. Gordon > Thank you very much in advance, > > Moritz > > -- output of sessionInfo(): > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel splines stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.20.0 > [5] BiocGenerics_0.6.0 statmod_1.4.17 edgeR_3.2.3 limma_3.16.5 > > loaded via a namespace (and not attached): > [1] annotate_1.38.0 AnnotationDbi_1.22.6 compiler_3.0.1 > [4] DBI_0.2-7 genefilter_1.42.0 geneplotter_1.38.0 > [7] grid_3.0.1 IRanges_1.18.1 RColorBrewer_1.0-5 > [10] RSQLite_0.11.4 stats4_3.0.1 survival_2.37-4 > [13] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 > > > -- ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}